Sequencing results analysis - (Jul/17/2009 )

I'm currently doing a lot of site-directed mutagenesis by an approach based on whole plasmid PCR amplification, and I need to verify the sequence of the supposedly mutated plasmids I generated. Basically, what I'd need is a software that would allow the following steps of analysis:

1) Enter a multiple sequence data set
2) Reverse-complement sequences
3) Perform a multiple alignment (to locate mutations and verify integrity of vector sequences required for further expression of mutated gene)
4) Edit alignment so that I can highlight expression sequences of the vector and position of mutations (for instances by changing the background color of columns or boxes)

Is there a software that allows this, or am I dreaming ?
I know how to run steps 1-3 separately (or together with Bioedit), but I don't know how to do step 4.

Thanks for your help !

Seb

-sebinou-

Hi,
Have a look at CodonCode Aligner (http://www.codoncode.com/). You can drag and drop .abi (quality) files and reference sequences. It will align, highlight, screen for mismatches and open the raw sequence files for your pleasure. The 30days full trial and demo version is free of charge (Unfortunately, no print/save in the demo, but you can make a screen shot ). I really love it!
Cheers,
Minna